Nothing
f.extract.freq <- function( data, alleles.orig, design ){
freq.x <- NULL
nas.x <- NULL
if( !is.null( data$cov.data ) ){
## GET FREQUENCY COUNT FOR COVARIATE DATA
tmp <- lapply( 1:ncol( data$cov.data ), function(i) f.freq.table( unlist( data$cov.data[,i] ) ) )
names( tmp ) <- colnames( data$cov.data )
freq.x <- lapply( tmp, function(x) x$tab )
nas.x <- sapply( tmp, function(x) x$nas )
}
if( design %in% c( "triad", "cc.triad" ) ) {
tt <- 6
}else if( design == "cc" ) tt <- 2
marker.seq <- 1:( ncol( data$gen.data ) / tt )
alleles.freq <- sapply( marker.seq, function( i ){
list( f.freq.table( data$gen.data[ ,( (i-1)*tt + 1 ):( i*tt ) ] ) )
} )
names( alleles.freq ) <- names( alleles.orig )
alleles.new <- lapply( 1:length( alleles.freq ), function(x){
freq.tmp <- alleles.freq[[x]]$tab
names( freq.tmp ) <- names( alleles.orig[[x]] )[ as.numeric( names( freq.tmp ) ) ]
return( freq.tmp )
})
names( alleles.new ) <- names( alleles.orig )
alleles.nas.new <- lapply( alleles.freq, function(x) x$nas )
return( list( variables = freq.x, variables.nas = nas.x, alleles = alleles.new, alleles.nas = alleles.nas.new ) )
}
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